Rampant speculation concerning the Halo story.
Yes, I came up with this in the shower.
Yes, it's 1:30 AM.
Yes, I'm tired.
No, no drugs.

The Forerunner had been for all of known history the dominant race in the galaxy in which they resided. They were a relatively peaceful, highly intelligent form of life which were viewed as Gods by the other, less evolved creatures that occupied planets on the outer edges of the star system. They were especially skilled in the practices of space travel and bio-engineering.

The Forerunner were so advanced in space travel that they had gone so far as to experiment with the construction of their own planet-like stations: artificially constructed worlds that could be used as places of residence should a population be required to relocate due to overpopulation. They built three types of stations: Residential Stations, Industrial Stations, and Fortress Stations.

Residential Stations were the main worlds where the Forerunner lived. These worlds included housing and shopping accomodations enough for their maximum population base. Many of the Forerunner that lived on these Residential Stations would find work in the local shopping centers which were always open. These Stations were most often spherical and the occupants dwelled on the outside surface, much like standard planets.

Industrial Stations were where research and development of new technologies occurred. The smartest of the Forerunner often found employ on these worlds and were tasked with finding more efficient tools, more entertaining toys, and more powerful vaccines for illness. These stations were most often spherical but unlike Residential Stations, the occupants lived on the inside of the sphere.

Fortress Stations were seldom manned because of the peaceful nature of the Forerunner. However, they weren't completely positive that they wouldn't encounter a warrior race equally or perhaps even more powerful than they were so they built them all the same. They had artificial intelligence cybernetic watchers that kept tabs on all that occurred on the Fortres Worlds. These worlds were most often ring-shaped and the occupants resided on the inner surface of the ring.

For ages and ages the Forerunner lived in peace in their galaxy, making marvelous new discoveries and thriving on what they learned. They were at the peak of their civilization. Then, a plague hit the Forerunner populace. Thousands of them took ill and died. Many Forerunner were hospitalized to no avail and the doctors that treated them got sick soon after.

The bio-engineering section of the Forerunner Industry was contracted to create an artificial vaccine for the disease. Within a very short time, they called for one million volunteers from the population to test their new vaccine. The donor list soon filled up and the donors crowded the testing facilities of the Industrial Station as the vaccine was administered. The Forerunner populace waited in suspense. A reply came in the form of transport shuttles returning from the Industrial Station: either filled with cured Forerunner or decaying corpses of a failed attempt. Or so they thought.

They thought incorrectly.

As the shuttles entered the landing bays of their respective worlds, the doors burst open and creatures that had never before been seen poured out, killing anyone that they immediately saw. Those killed almost immediately began to transform, seeming to decay into a new form of life before they themselves rose and aided in the attack.

Entire Stations were consumed and the parasitic creatures used the plethora of shuttles on each station to spread even further. Few escaped.

One of those that did escape sent a message to the High Government of the Forerunner informing them of the threat. The Government held council and came to a consensus to send a wide-band signal throughout the galaxy asking all intelligence that may recieve it to fight the parasitic threat.

The Governmental Station was overrun shortly thereafter.

A few scientists did manage to aquire a sample of the parasite and transported it to one of their most remote Fortress Stations so that they could study it and possibly come upon a cure for this Forerunner-Created disease without the immediate threat of being overrun by the parasite. Any scientists that were available lended their intelligence to the research. However, a careless mistake led to a breakout of the disease on the station itself. One Forerunner Scientist saw that they had run out of options: there was only one thing left to do.

Each Fortress World was built around a central weapon that would wipe out all life within a specified radius from the station dependant on how large the Fortress World was. After the weapon was fired, a signal would be sent to all other Fortress Stations in the galaxy and unless the process was cancelled by a Fortress Operator, they too would go off. The stations were positioned in such a way that if they all were fired, the entire galaxy would essentially be stripped clean of life. To further ensure the total destruction of life, all of the Residential and Industrial Stations were rigged to self-destruct themselves if they were within a firing Fortress World's effective radius.

Back to the Scientist from two paragraphs ago. He, wearing a completely self-contained environmental suit, retrieved the Index from the Fortress Station's Library with the help of the station's Monitor. The Monitor teleported himself and the Scientist to the Control Room and the Scientist hesitated.

"Is there anything else we can do? Is there something we haven't tried?" the Scientist asked the Monitor. "If you were in my position, would you do it?"

"From the data I have, I can see no other course of action," the Monitor replied coldly.

The Scientist took one last look around the Control Room of the Station, glanced down at the Index in his hand, and inserted it into the firing mechanism in the Station's Control Room.

The resulting series of events ended all life in that galaxy. Except, by chance, the orbit of one of the Stations around its star pulled it just far enough away from one edge of the galaxy so that the ends of two of the spiral arms were left just outside of the blast radius.

Luckily, the life in these sections of the galaxy were uninfected by the Forerunner Virus. One group of organisms were even far enough along in their evolution that they recieved the transmission from the Forerunner, higher beings that they viewed as Gods, to "Destroy the Parasitic Creatures". They immediately began scouring the galaxy, looking for the parasites. Through their search they came upon other, less evolved creatures and absorbed all of the less evolved into their culture.

They had started searching away from the second spiral arm that had been outside of the cataclysmic event. Unfortunately in this arm, only one tiny corner had been undestroyed. One form of life remained in this arm and they began developing at a very fast rate. Before too long, they had colonized worlds extending far out from their original planet.

Unfortunately for them, their radio recievers had been invented seven years too late to intercept the Forerunner transmission. They had no idea that there were other forms of intelligent life in their galaxy.

Had the conglomeration of races from the first arm of the galaxy (which called itself the Covenant) started their search in the arm that contained this lesser evolved race, perhaps things would've turned out differently when the two first encountered each other. Instead of coming upon a culture that had seemingly taken over hundereds of worlds crushing the life that had been there before, the Covenant might have come upon a species that had just learned how to send rockets into space. Thus, the Covenant might not have mistaken the Humans for the Parasites that the Forerunner transmission urged them to destroy.

However, the Covenant did not know that the true parasite was still alive, locked deep within the Fortress world that was used as a last effort to save the race that inadvertently destroyed itself with one of its own creations.